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- PDB-1t0d: Crystal Structure of 2-aminopurine labelled bacterial decoding si... -

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Basic information

Entry
Database: PDB / ID: 1t0d
TitleCrystal Structure of 2-aminopurine labelled bacterial decoding site RNA
Components
  • 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'
  • 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'
KeywordsRNA / 2-AMINOPURINE / BACTERIAL DECODING SITE RNA / FLUORESCENCE EMISSION SPECTRA / 9-beta-D-Ribofuranosyl-9H-purin-2-amine
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShandrick, S. / Zhao, Q. / Han, Q. / Ayida, B.K. / Takahashi, M. / Winters, G.C. / Simonsen, K.B. / Vourloumis, D. / Hermann, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2004
Title: Monitoring molecular recognition of the ribosomal decoding site.
Authors: Shandrick, S. / Zhao, Q. / Han, Q. / Ayida, B.K. / Takahashi, M. / Winters, G.C. / Simonsen, K.B. / Vourloumis, D. / Hermann, T.
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'
B: 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'
C: 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'
D: 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)21,1414
Polymers21,1414
Non-polymers00
Water3,873215
1
A: 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'
B: 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,5702
Polymers10,5702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'
D: 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)10,5702
Polymers10,5702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.640, 87.320, 32.790
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*GP*UP*GP*(MTU)P*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'


Mass: 5555.333 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*AP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'


Mass: 5015.079 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium sulfate, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2003 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 8984 / Num. obs: 8903 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.3 / Num. unique all: 844 / % possible all: 96.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a model of RNA

Resolution: 2.2→8 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 870 -RANDOM
Rwork0.205 ---
all-8867 --
obs-8285 93.4 %-
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å20 Å20.408 Å2
2--5.144 Å20 Å2
3----1.183 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1398 0 215 1613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.93
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.354 129 -
Rwork0.308 --
obs--82.4 %

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